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      Drug-resistant tuberculosis: challenges and opportunities for diagnosis and treatment

      review-article
      1 , 2 , 2 , 1 , 2
      Current Opinion in Pharmacology
      Elsevier Science Ltd

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          Graphical abstract

          Highlights

          • Management of tuberculosis is complicated by high levels of drug resistance in some regions of the world.

          • Increasingly, molecular diagnostics are being used for resistance detection to certain first-line anti-TB drugs.

          • Genotype-phenotype relationships for resistance to other drugs are complex making DST by molecular methods challenging.

          • Individualized approaches to MDR-TB treatment management may help to minimize the development of further resistance.

          • Individualized approaches to MDR-TB treatment management may help to minimize the development of further resistance.

          Abstract

          With an estimated incidence of 490 000 cases in 2016, multidrug resistant tuberculosis (TB), against which key first-line anti-tuberculars are less efficacious, presents major challenges for global health. Poor treatment outcomes coupled with a yawning treatment gap between those in need of second-line therapy and those who receive it, underscore the urgent need for new approaches to tackle the scourge of drug-resistant TB. Against this background, significant progress has been made in understanding the complex biology of TB drug resistance and disease pathogenesis, and in establishing a pipeline for delivering new drugs and drug combinations. In this review, we highlight the challenges of drug-resistant TB and the ways in which new advances could be harnessed to improve treatment outcomes.

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          Most cited references47

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          Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis

          The rise of antibiotic-resistant bacteria has led to an urgent need for rapid detection of drug resistance in clinical samples, and improvements in global surveillance. Here we show how de Bruijn graph representation of bacterial diversity can be used to identify species and resistance profiles of clinical isolates. We implement this method for Staphylococcus aureus and Mycobacterium tuberculosis in a software package (‘Mykrobe predictor') that takes raw sequence data as input, and generates a clinician-friendly report within 3 minutes on a laptop. For S. aureus, the error rates of our method are comparable to gold-standard phenotypic methods, with sensitivity/specificity of 99.1%/99.6% across 12 antibiotics (using an independent validation set, n=470). For M. tuberculosis, our method predicts resistance with sensitivity/specificity of 82.6%/98.5% (independent validation set, n=1,609); sensitivity is lower here, probably because of limited understanding of the underlying genetic mechanisms. We give evidence that minor alleles improve detection of extremely drug-resistant strains, and demonstrate feasibility of the use of emerging single-molecule nanopore sequencing techniques for these purposes.
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            Tuberculosis Drug Resistance Mutation Database

            Andreas Sandgren and colleagues describe a new comprehensive resource on drug resistance mutations inM. tuberculosis.
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              PhyResSE: a Web Tool Delineating Mycobacterium tuberculosis Antibiotic Resistance and Lineage from Whole-Genome Sequencing Data.

              Antibiotic-resistant tuberculosis poses a global threat, causing the deaths of hundreds of thousands of people annually. While whole-genome sequencing (WGS), with its unprecedented level of detail, promises to play an increasingly important role in diagnosis, data analysis is a daunting challenge. Here, we present a simple-to-use web service (free for academic use at http://phyresse.org). Delineating both lineage and resistance, it provides state-of-the-art methodology to life scientists and physicians untrained in bioinformatics. It combines elaborate data processing and quality control, as befits human diagnostics, with a treasure trove of validated resistance data collected from well-characterized samples in-house and worldwide.
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                Author and article information

                Contributors
                Journal
                Curr Opin Pharmacol
                Curr Opin Pharmacol
                Current Opinion in Pharmacology
                Elsevier Science Ltd
                1471-4892
                1471-4973
                1 October 2018
                October 2018
                : 42
                : 7-15
                Affiliations
                [1 ]SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical TB Research and Wellcome Centre for Clinical Infectious Diseases Research in Africa, University of Cape Town, South Africa
                [2 ]Institute of Infectious Disease and Molecular Medicine and Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, South Africa
                Article
                S1471-4892(17)30157-1
                10.1016/j.coph.2018.05.013
                6219890
                29885623
                841fcbef-9cde-4f7c-aa89-4157f27645c0
                © 2018 The Authors

                This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

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                Categories
                Article

                Pharmacology & Pharmaceutical medicine
                Pharmacology & Pharmaceutical medicine

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